chore(release): 🔖 version 0.15.0

Makefile

@@ -185,7 +185,8 @@ permissions: certs
 		prometheus.dev.yml \
 		settings.conf \
 		tests/config/registries/seek/nginx.conf \
-		tests/config/registries/seek/doorkeeper.rb
+		tests/config/registries/seek/doorkeeper.rb \
+	&& mkdir -p /tmp/lifemonitor-logs
 
 
 aux_images: tests/config/registries/seek/seek.Dockerfile certs
@@ -223,7 +224,8 @@ start-dev: images compose-files dev reset_compose permissions ## Start LifeMonit
 start-testing: compose-files aux_images ro_crates images reset_compose permissions ## Start LifeMonitor in a Testing environment
 	@printf "\n$(bold)Starting testing services...$(reset)\n" ; \
 	base=$$(if [[ -f "docker-compose.yml" ]]; then echo "-f docker-compose.yml"; fi) ; \
-	echo "$$($(docker_compose) $${base} \
+	echo "$$(USER_UID=$$(id -u) USER_GID=$$(id -g) \
+			$(docker_compose) $${base} \
 				-f docker-compose.extra.yml \
 				-f docker-compose.base.yml \
 				-f docker-compose.monitoring.yml \

docker-compose.base.yml

@@ -1,5 +1,3 @@
-version: "3.5"
-
 services:
   db:
     # Docker image docs: https://github.com/bitnami/bitnami-docker-postgresql
@@ -65,6 +63,7 @@ services:
       - "./instance:/lm/instance:ro"
       - "./settings.conf:/lm/settings.conf:ro" # default settings
       - "data_workflows:/var/data/lm"
+      - "/tmp/lifemonitor-logs:/var/log/lm"
     networks:
       - life_monitor
 

docker-compose.dev.yml

@@ -1,5 +1,3 @@
-version: "3.5"
-
 services:
   db:
     environment:

docker-compose.extra.yml

@@ -1,5 +1,3 @@
-version: "3.5"
-
 services:
   seek:
     image: crs4/lifemonitor-tests:seek

docker-compose.maintenance.yml

@@ -0,0 +1,61 @@
+services:
+  db:
+    environment:
+      - "ALLOW_EMPTY_PASSWORD=yes"
+
+  console:
+    image: crs4/lifemonitor
+    restart: "unless-stopped"
+    depends_on:
+      - "db"
+      - "init"
+      - "redis"
+    entrypoint: /bin/bash
+    command: |
+      -c "sleep infinity"
+    user: "${USER_UID}:${USER_GID}"
+    env_file:
+      - settings.conf
+    environment:
+      - "FLASK_ENV=development"
+      - "TEMPLATES_AUTO_RELOAD=True"
+      - "HOME=/lm"
+      # Normally, OAuthLib will raise an InsecureTransportError if you attempt to use OAuth2 over HTTP,
+      # rather than HTTPS. Setting this environment variable will prevent this error from being raised.
+      # This is mostly useful for local testing, or automated tests. Never set this variable in production.
+      - "AUTHLIB_INSECURE_TRANSPORT=1"
+      # - "SERVER_NAME=lm:8000"
+    volumes:
+      - "./certs:/certs:ro"
+      - "./instance:/lm/instance:ro"
+      - "./settings.conf:/lm/settings.conf:ro" # default settings
+      - "./:/lm"
+      - "data_workflows:/var/data/lm"
+    ports:
+      - "8000"
+    networks:
+      - life_monitor
+
+  init:
+    user: "${USER_UID}:${USER_GID}"
+    environment:
+      - "FLASK_ENV=development"
+      # Normally, OAuthLib will raise an InsecureTransportError if you attempt to use OAuth2 over HTTP,
+      # rather than HTTPS. Setting this environment variable will prevent this error from being raised.
+      # This is mostly useful for local testing, or automated tests. Never set this variable in production.
+      - "AUTHLIB_INSECURE_TRANSPORT=1"
+      - "HOME=/lm"
+    volumes:
+      - "./:/lm"
+
+  lm:
+    environment:
+      - "FLASK_ENV=maintenance"
+
+  ws_server:
+    environment:
+      - "FLASK_ENV=maintenance"
+
+  worker:
+    environment:
+      - "FLASK_ENV=maintenance"

docker-compose.monitoring.yml

@@ -1,5 +1,3 @@
-version: "3.5"
-
 services:
   prometheus:
     image: prom/prometheus:v2.48.0

docker-compose.test.yml

@@ -1,5 +1,3 @@
-version: "3.5"
-
 services:
   lmtests:
     image: crs4/lifemonitor
@@ -34,6 +32,7 @@ services:
       - "./certs:/certs:ro"
       - "./instance:/lm/instance:ro"
       - "./settings.conf:/lm/settings.conf:ro" # default settings
+      - "/tmp/lifemonitor-logs:/var/log/lm"
     ports:
       - "8000"
     networks:

docker/lifemonitor.Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.10-slim-buster as base
+FROM python:3.10-slim-buster AS base
 
 # Install base requirements
 RUN apt-get update -q \
@@ -100,7 +100,7 @@ RUN find /lm/lifemonitor/ -type d -exec chmod a+r {} \;
 ##################################################################
 ## Node Stage
 ##################################################################
-FROM node:14.16.0-alpine3.12 as node
+FROM node:14.16.0-alpine3.12 AS node
 
 
 RUN mkdir -p /static && apk add --no-cache bash python3 make g++ \
@@ -119,7 +119,7 @@ RUN npm run production
 ##################################################################
 ## Target Stage
 ##################################################################
-FROM base as target
+FROM base AS target
 
 # Set software and build number
 ARG SW_VERSION

docker/worker_entrypoint.sh

@@ -41,9 +41,10 @@ export dramatiq_prom_db="${PROMETHEUS_MULTIPROC_DIR}"
 log "Starting task queue worker container"
 debug_log "PROMETHEUS_MULTIPROC_DIR = ${PROMETHEUS_MULTIPROC_DIR}"
 
-if [[ -n "${DEBUG:-}" ]]; then
+verbose=""
+if [[ -n "${VERBOSE:-}" ]]; then
   verbose='--verbose'
-  log "Debug Mode Enabled"
+  echo "Verbose Mode Enabled"
 fi
 
 if [[ ${FLASK_ENV} == "development" ]]; then
@@ -94,4 +95,4 @@ done
 
 log "Worker exiting with exit code ${exit_code}"
 
-exit ${exit_code}
+exit ${exit_code}

k8s/Chart.yaml

@@ -12,7 +12,7 @@ version: 0.12.0
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application. Versions are not expected to
 # follow Semantic Versioning. They should reflect the version the application is using.
-appVersion: 0.14.0
+appVersion: 0.15.0
 
 # Chart dependencies
 dependencies:

k8s/templates/backup.job.yaml

@@ -1,5 +1,5 @@
 {{- if .Values.backup.enabled -}}
-apiVersion: batch/v1beta1
+apiVersion: batch/v1
 kind: CronJob
 metadata:
   name: {{ include "chart.fullname" . }}-backup
@@ -58,4 +58,4 @@ spec:
             {{- toYaml . | nindent 10 }}        
           {{- end }}
       backoffLimit: 4
-{{- end }}
+{{- end }}

k8s/templates/data-backup.pvc.yaml

@@ -5,6 +5,8 @@ kind: PersistentVolumeClaim
 metadata:
   name: {{ include "chart.lifemonitor.data.backup" . }}
   namespace: {{ .Release.Namespace }}
+  annotations:
+    "helm.sh/resource-policy": keep
 spec:
   storageClassName: {{ .Values.global.readWriteManyStorageClass }}
   accessModes:

k8s/templates/data-workflows.pvc.yaml

@@ -5,6 +5,8 @@ kind: PersistentVolumeClaim
 metadata:
   name: {{ include "chart.lifemonitor.data.workflows" . }}
   namespace: {{ .Release.Namespace }}
+  annotations:
+    helm.sh/resource-policy: keep
 spec:
   storageClassName: {{ .Values.global.readWriteManyStorageClass }}
   accessModes:

k8s/templates/init.job.yaml

@@ -1,3 +1,4 @@
+{{- if not .Values.maintenanceMode.enabled -}}
 apiVersion: batch/v1
 kind: Job
 metadata:
@@ -47,3 +48,4 @@ spec:
         {{- toYaml . | nindent 8 }}        
       {{- end }}
   backoffLimit: 4
+{{- end }}

k8s/values.yaml

@@ -288,15 +288,15 @@ worker:
     - name: github
       # image: *lifemonitorImage
     # - name: heartbeat
-      # image: *lifemonitorImage
+    #   image: *lifemonitorImage
     - name: notifications
       # image: *lifemonitorImage
     - name: builds
       # image: *lifemonitorImage
     - name: workflows
       # image: *lifemonitorImage
     # - name: metrics
-      # image: *lifemonitorImage
+    #   image: *lifemonitorImage
     - name: ws
       # image: *lifemonitorImage
 

lifemonitor/api/controllers.py

@@ -249,7 +249,9 @@ def registry_user_workflows_get(user_id, status=False, versions=False):
         workflows = lm.get_user_registry_workflows(identity.user, current_registry)
         logger.debug("registry_user_workflows_get. Got %s workflows (user: %s)", len(workflows), current_user)
         return serializers.ListOfWorkflows(workflow_status=status, workflow_versions=versions).dump(workflows)
-    except OAuthIdentityNotFoundException:
+    except OAuthIdentityNotFoundException as e:
+        if logger.isEnabledFor(logging.DEBUG):
+            logger.exception(e)
         return lm_exceptions.report_problem(401, "Unauthorized",
                                             detail=messages.no_user_oauth_identity_on_registry
                                             .format(user_id, current_registry.name))

lifemonitor/api/models/repositories/config.py

@@ -150,7 +150,11 @@ def registries(self) -> List[models.WorkflowRegistry]:
         for rfs in self._get_refs_list():
             for r in rfs.get("update_registries", []):
                 if not registries.get(r, None):
-                    registries[r] = models.WorkflowRegistry.find_by_client_name(r)
+                    r_model = models.WorkflowRegistry.find_by_client_name(r)
+                    if r_model is None:
+                        logger.warning("Unable to find registry: %r", r)
+                    else:
+                        registries[r] = r_model
         return list(registries.values())
 
     def get_ref_registries(self, ref_type: str, tag: str) -> List[models.WorkflowRegistry]:

lifemonitor/api/services.py

@@ -626,7 +626,8 @@ def find_registry_user_identity(registry: models.WorkflowRegistry,
             raise ValueError("external_id and internal_id cannot be both None")
         if internal_id:
             return OAuthIdentity.find_by_user_id(internal_id, registry.name)
-        return OAuthIdentity.find_by_provider_user_id(external_id, registry.name)
+        assert registry, "The registry should be defined"
+        return OAuthIdentity.find_by_provider_user_id(external_id, registry.client_name)
 
     @staticmethod
     def add_workflow_registry(type, name,

lifemonitor/static/src/package.json

@@ -1,7 +1,7 @@
 {
     "name": "lifemonitor",
     "description": "Workflow Testing Service",
-    "version": "0.14.0",
+    "version": "0.15.0",
     "license": "MIT",
     "author": "CRS4",
     "main": "../dist/js/lifemonitor.min.js",

requirements.txt

@@ -1,61 +1,59 @@
-Authlib~=0.15.4
-apscheduler==3.10.1
-connexion[swagger-ui]~=2.14.2
-dramatiq[redis,watch]==1.14.2
-email-validator~=1.1.3
-boto3~=1.24.80
+Authlib~=0.15.6
+apscheduler==3.10.4
+boto3~=1.35.9
 Bcrypt-Flask==1.0.2
-giturlparse~=0.10.0
 click-option-group~=0.5.5
+connexion[swagger-ui]~=2.14.2
 cryptography>=41.0.3
 dnspython==2.6.1
-flask-cors==3.0.10
-flask-marshmallow~=0.14.0
-flask-restful==0.3.9
+dramatiq[redis,watch]==1.14.2
+email-validator~=2.2.0
+eventlet==0.36.1
+flask-cors==4.0.1
 flask-login~=0.6.2
+flask-marshmallow~=0.14.0
+flask-restful==0.3.10
 flask-shell-ipython==0.5.1
-flask-wtf~=1.1.1
-Flask-APScheduler==1.12.4
+flask-wtf~=1.2.0
+Flask-APScheduler==1.13.1
+Flask-Mail~=0.10.0
+Flask-Migrate==4.0.7
 Flask-SQLAlchemy==2.5.1
-Flask-Migrate==3.1.0
-Flask-Mail~=0.9.1
 Flask~=2.2.5
-gunicorn~=20.1.0
-itsdangerous~=2.1.0
+flask-socketio==5.3.6
+gevent-websocket==0.10.1
+giturlparse~=0.12.0
+gunicorn~=23.0.0
+itsdangerous~=2.2.0
 jwt==1.3.1
-jsonschema==3.2.0
+jsonschema==4.23.0
 loginpass==0.5
 marshmallow-sqlalchemy~=0.28.2
+networkx~=3.3
 nf-core~=2.5.0
+pika~=1.3.2
 prometheus-flask-exporter~=0.22
-pygit2~=1.12.1
 psycopg2-binary~=2.9.6
-pyopenssl==23.2.0
-pytest-mock~=3.11.1
+pygit2~=1.15.1
+pyopenssl==24.2.1
 pytest~=7.4.0
+pytest-mock~=3.11.1
 pytest-rerunfailures~=12.0.0
 pytest-xdist~=3.3.1
-python-dotenv~=0.19.0
+python-dotenv~=1.0.1
 python-jenkins==1.7.0
 python-redis-lock~=4.0.0
 PyGithub==1.55
 PyYAML~=6.0.1
-pika~=1.2.0
 redis~=4.5.5
+repo2rocrate~=0.1.2
 requests~=2.31.0
+rich~=13.8.0
+rocrate==0.10.0
 snakemake==6.13.1
-networkx~=3.1.0
-rich~=13.4.1
-rocrate==0.8.0
 SQLAlchemy==1.4.41
-wheel~=0.40.0
+urllib3==1.26.19
+uwsgi==2.0.26
+watchdog==4.0.2
+wheel~=0.44.0
 Werkzeug~=2.2.3
-repo2rocrate~=0.1.2
-urllib3==1.26.18
-flask-socketio==5.3.4
-gevent-websocket==0.10.1
-eventlet==0.35.2
-uwsgi==2.0.22
-# watchdog version 2.3 introduces a change that breaks Flask in development mode.
-# Don't use watchdog > 2.2.1 until up update Flask to something >= 2.2
-watchdog==2.2.1

specs/api.yaml

@@ -3,7 +3,7 @@
 openapi: "3.0.0"
 
 info:
-  version: "0.14.0"
+  version: "0.15.0"
   title: "Life Monitor API"
   description: |
     *Workflow sustainability service*
@@ -18,7 +18,7 @@ info:
 servers:
   - url: /
     description: >
-      Version 0.14.0 of API.
+      Version 0.15.0 of API.
 
 tags:
   - name: GitHub Integration